Bringing Reduce Reads bug fixes to the main repository
This commit is contained in:
Mauricio Carneiro
commit
131cb7effd
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@ -12,7 +12,9 @@ if ( onCMDLine ) {
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inputFileName = args[1]
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outputPDF = args[2]
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} else {
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inputFileName = "~/Desktop/broadLocal/GATK/unstable/report.txt"
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#inputFileName = "~/Desktop/broadLocal/GATK/unstable/report.txt"
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inputFileName = "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/Q-25718@node1149.jobreport.txt"
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#inputFileName = "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/rodPerformanceGoals/history/report.082711.txt"
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outputPDF = NA
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}
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@ -113,11 +115,22 @@ plotGroup <- function(groupTable) {
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textplot(as.data.frame(sum), show.rownames=F)
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title(paste("Job summary for", name, "itemizing each iteration"), cex=3)
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# histogram of job times by groupAnnotations
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if ( length(groupAnnotations) == 1 && dim(sub)[1] > 1 ) {
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# todo -- how do we group by annotations?
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p <- ggplot(data=sub, aes(x=runtime)) + geom_histogram()
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p <- p + xlab("runtime in seconds") + ylab("No. of jobs")
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p <- p + opts(title=paste("Job runtime histogram for", name))
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print(p)
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}
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# as above, but averaging over all iterations
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groupAnnotationsNoIteration = setdiff(groupAnnotations, "iteration")
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sum = cast(melt(sub, id.vars=groupAnnotationsNoIteration, measure.vars=c("runtime")), ... ~ ., fun.aggregate=c(mean, sd))
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textplot(as.data.frame(sum), show.rownames=F)
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title(paste("Job summary for", name, "averaging over all iterations"), cex=3)
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if ( dim(sub)[1] > 1 ) {
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sum = cast(melt(sub, id.vars=groupAnnotationsNoIteration, measure.vars=c("runtime")), ... ~ ., fun.aggregate=c(mean, sd))
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textplot(as.data.frame(sum), show.rownames=F)
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title(paste("Job summary for", name, "averaging over all iterations"), cex=3)
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}
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}
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# print out some useful basic information
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@ -146,7 +159,7 @@ plotJobsGantt(gatkReportData, T)
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plotJobsGantt(gatkReportData, F)
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plotProgressByTime(gatkReportData)
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for ( group in gatkReportData ) {
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plotGroup(group)
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plotGroup(group)
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}
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if ( ! is.na(outputPDF) ) {
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@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.refdata;
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import net.sf.samtools.util.SequenceUtil;
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import org.broad.tribble.Feature;
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import org.broad.tribble.annotation.Strand;
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import org.broad.tribble.dbsnp.DbSNPFeature;
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import org.broad.tribble.dbsnp.OldDbSNPFeature;
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import org.broad.tribble.gelitext.GeliTextFeature;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.utils.classloader.PluginManager;
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@ -93,27 +93,27 @@ public class VariantContextAdaptors {
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// --------------------------------------------------------------------------------------------------------------
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private static class DBSnpAdaptor implements VCAdaptor {
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private static boolean isSNP(DbSNPFeature feature) {
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private static boolean isSNP(OldDbSNPFeature feature) {
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return feature.getVariantType().contains("single") && feature.getLocationType().contains("exact");
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}
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private static boolean isMNP(DbSNPFeature feature) {
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private static boolean isMNP(OldDbSNPFeature feature) {
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return feature.getVariantType().contains("mnp") && feature.getLocationType().contains("range");
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}
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private static boolean isInsertion(DbSNPFeature feature) {
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private static boolean isInsertion(OldDbSNPFeature feature) {
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return feature.getVariantType().contains("insertion");
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}
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private static boolean isDeletion(DbSNPFeature feature) {
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private static boolean isDeletion(OldDbSNPFeature feature) {
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return feature.getVariantType().contains("deletion");
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}
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private static boolean isIndel(DbSNPFeature feature) {
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private static boolean isIndel(OldDbSNPFeature feature) {
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return isInsertion(feature) || isDeletion(feature) || isComplexIndel(feature);
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}
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public static boolean isComplexIndel(DbSNPFeature feature) {
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public static boolean isComplexIndel(OldDbSNPFeature feature) {
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return feature.getVariantType().contains("in-del");
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}
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@ -125,7 +125,7 @@ public class VariantContextAdaptors {
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*
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* @return an alternate allele list
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*/
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public static List<String> getAlternateAlleleList(DbSNPFeature feature) {
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public static List<String> getAlternateAlleleList(OldDbSNPFeature feature) {
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List<String> ret = new ArrayList<String>();
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for (String allele : getAlleleList(feature))
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if (!allele.equals(String.valueOf(feature.getNCBIRefBase()))) ret.add(allele);
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@ -139,7 +139,7 @@ public class VariantContextAdaptors {
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*
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* @return an alternate allele list
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*/
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public static List<String> getAlleleList(DbSNPFeature feature) {
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public static List<String> getAlleleList(OldDbSNPFeature feature) {
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List<String> alleleList = new ArrayList<String>();
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// add ref first
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if ( feature.getStrand() == Strand.POSITIVE )
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@ -156,14 +156,14 @@ public class VariantContextAdaptors {
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/**
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* Converts non-VCF formatted dbSNP records to VariantContext.
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* @return DbSNPFeature.
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* @return OldDbSNPFeature.
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*/
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@Override
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public Class<? extends Feature> getAdaptableFeatureType() { return DbSNPFeature.class; }
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public Class<? extends Feature> getAdaptableFeatureType() { return OldDbSNPFeature.class; }
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@Override
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public VariantContext convert(String name, Object input, ReferenceContext ref) {
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DbSNPFeature dbsnp = (DbSNPFeature)input;
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OldDbSNPFeature dbsnp = (OldDbSNPFeature)input;
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if ( ! Allele.acceptableAlleleBases(dbsnp.getNCBIRefBase()) )
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return null;
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Allele refAllele = Allele.create(dbsnp.getNCBIRefBase(), true);
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@ -26,8 +26,11 @@ package org.broadinstitute.sting.gatk.refdata.tracks;
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import net.sf.samtools.SAMSequenceDictionary;
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import net.sf.samtools.util.CloseableIterator;
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import org.apache.log4j.Logger;
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import org.broad.tribble.Feature;
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import org.broad.tribble.FeatureCodec;
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import org.broad.tribble.FeatureSource;
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import org.broad.tribble.iterators.CloseableTribbleIterator;
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import org.broad.tribble.source.PerformanceLoggingFeatureSource;
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import org.broadinstitute.sting.gatk.refdata.utils.FeatureToGATKFeatureIterator;
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import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
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import org.broadinstitute.sting.utils.GenomeLoc;
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@ -47,7 +50,6 @@ import java.io.IOException;
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*/
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public class RMDTrack {
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private final static Logger logger = Logger.getLogger(RMDTrackBuilder.class);
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private final static boolean DEBUG = false;
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// the basics of a track:
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private final Class type; // our type
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@ -113,8 +115,10 @@ public class RMDTrack {
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}
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public CloseableIterator<GATKFeature> query(GenomeLoc interval) throws IOException {
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if ( DEBUG ) logger.debug("Issuing query for %s: " + interval);
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return new FeatureToGATKFeatureIterator(genomeLocParser, reader.query(interval.getContig(),interval.getStart(),interval.getStop()), this.getName());
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CloseableTribbleIterator<Feature> iter = reader.query(interval.getContig(),interval.getStart(),interval.getStop());
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if ( RMDTrackBuilder.MEASURE_TRIBBLE_QUERY_PERFORMANCE )
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logger.warn("Query " + getName() + ":" + ((PerformanceLoggingFeatureSource)reader).getPerformanceLog());
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return new FeatureToGATKFeatureIterator(genomeLocParser, iter, this.getName());
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}
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public void close() {
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@ -27,20 +27,21 @@ package org.broadinstitute.sting.gatk.refdata.tracks;
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import net.sf.samtools.SAMSequenceDictionary;
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import net.sf.samtools.SAMSequenceRecord;
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import org.apache.log4j.Logger;
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import org.broad.tribble.*;
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import org.broad.tribble.FeatureCodec;
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import org.broad.tribble.FeatureSource;
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import org.broad.tribble.Tribble;
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import org.broad.tribble.TribbleException;
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import org.broad.tribble.index.Index;
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import org.broad.tribble.index.IndexFactory;
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import org.broad.tribble.source.BasicFeatureSource;
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import org.broad.tribble.source.PerformanceLoggingFeatureSource;
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import org.broad.tribble.util.LittleEndianOutputStream;
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import org.broadinstitute.sting.commandline.Tags;
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import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
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import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
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import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
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import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.SequenceDictionaryUtils;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.utils.classloader.PluginManager;
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import org.broadinstitute.sting.utils.collections.Pair;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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@ -51,7 +52,10 @@ import org.broadinstitute.sting.utils.instrumentation.Sizeof;
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import java.io.File;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.util.*;
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import java.util.LinkedHashSet;
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import java.util.Map;
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import java.util.Set;
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import java.util.TreeSet;
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@ -70,6 +74,7 @@ public class RMDTrackBuilder { // extends PluginManager<FeatureCodec> {
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* our log, which we use to capture anything from this class
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*/
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private final static Logger logger = Logger.getLogger(RMDTrackBuilder.class);
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public final static boolean MEASURE_TRIBBLE_QUERY_PERFORMANCE = false;
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// a constant we use for marking sequence dictionary entries in the Tribble index property list
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public static final String SequenceDictionaryPropertyPredicate = "DICT:";
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@ -214,7 +219,10 @@ public class RMDTrackBuilder { // extends PluginManager<FeatureCodec> {
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sequenceDictionary = getSequenceDictionaryFromProperties(index);
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}
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featureSource = new BasicFeatureSource(inputFile.getAbsolutePath(), index, createCodec(descriptor, name));
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if ( MEASURE_TRIBBLE_QUERY_PERFORMANCE )
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featureSource = new PerformanceLoggingFeatureSource(inputFile.getAbsolutePath(), index, createCodec(descriptor, name));
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else
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featureSource = new BasicFeatureSource(inputFile.getAbsolutePath(), index, createCodec(descriptor, name));
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}
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catch (TribbleException e) {
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throw new UserException(e.getMessage());
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@ -105,10 +105,19 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
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@Multiplex(value=DoCOutputMultiplexer.class,arguments={"partitionTypes","refSeqGeneList","omitDepthOutput","omitIntervals","omitSampleSummary","omitLocusTable"})
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Map<DoCOutputType,PrintStream> out;
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/**
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* Sets the low-coverage cutoff for granular binning. All loci with depth < START are counted in the first bin.
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*/
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@Argument(fullName = "start", doc = "Starting (left endpoint) for granular binning", required = false)
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int start = 1;
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/**
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* Sets the high-coverage cutoff for granular binning. All loci with depth > END are counted in the last bin.
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*/
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@Argument(fullName = "stop", doc = "Ending (right endpoint) for granular binning", required = false)
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int stop = 500;
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/**
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* Sets the number of bins for granular binning
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*/
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@Argument(fullName = "nBins", doc = "Number of bins to use for granular binning", required = false)
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int nBins = 499;
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@Argument(fullName = "minMappingQuality", shortName = "mmq", doc = "Minimum mapping quality of reads to count towards depth. Defaults to -1.", required = false)
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@ -119,28 +128,59 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
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byte minBaseQuality = -1;
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@Argument(fullName = "maxBaseQuality", doc = "Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE).", required = false)
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byte maxBaseQuality = Byte.MAX_VALUE;
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/**
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* Instead of reporting depth, report the base pileup at each locus
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*/
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@Argument(fullName = "printBaseCounts", shortName = "baseCounts", doc = "Will add base counts to per-locus output.", required = false)
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boolean printBaseCounts = false;
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/**
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* Do not tabulate locus statistics (# loci covered by sample by coverage)
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*/
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@Argument(fullName = "omitLocusTable", shortName = "omitLocusTable", doc = "Will not calculate the per-sample per-depth counts of loci, which should result in speedup", required = false)
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boolean omitLocusTable = false;
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/**
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* Do not tabulate interval statistics (mean, median, quartiles AND # intervals by sample by coverage)
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*/
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@Argument(fullName = "omitIntervalStatistics", shortName = "omitIntervals", doc = "Will omit the per-interval statistics section, which should result in speedup", required = false)
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boolean omitIntervals = false;
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/**
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* Do not print the total coverage at every base
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*/
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@Argument(fullName = "omitDepthOutputAtEachBase", shortName = "omitBaseOutput", doc = "Will omit the output of the depth of coverage at each base, which should result in speedup", required = false)
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boolean omitDepthOutput = false;
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@Argument(fullName = "printBinEndpointsAndExit", doc = "Prints the bin values and exits immediately. Use to calibrate what bins you want before running on data.", required = false)
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boolean printBinEndpointsAndExit = false;
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/**
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* Do not tabulate the sample summary statistics (total, mean, median, quartile coverage per sample)
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*/
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@Argument(fullName = "omitPerSampleStats", shortName = "omitSampleSummary", doc = "Omits the summary files per-sample. These statistics are still calculated, so this argument will not improve runtime.", required = false)
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boolean omitSampleSummary = false;
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/**
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* A way of partitioning reads into groups. Can be sample, readgroup, or library.
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*/
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@Argument(fullName = "partitionType", shortName = "pt", doc = "Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library.", required = false)
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Set<DoCOutputType.Partition> partitionTypes = EnumSet.of(DoCOutputType.Partition.sample);
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/**
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* Consider a spanning deletion as contributing to coverage. Also enables deletion counts in per-base output.
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*/
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@Argument(fullName = "includeDeletions", shortName = "dels", doc = "Include information on deletions", required = false)
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boolean includeDeletions = false;
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@Argument(fullName = "ignoreDeletionSites", doc = "Ignore sites consisting only of deletions", required = false)
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boolean ignoreDeletionSites = false;
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/**
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* Path to the RefSeq file for use in aggregating coverage statistics over genes
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*/
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@Argument(fullName = "calculateCoverageOverGenes", shortName = "geneList", doc = "Calculate the coverage statistics over this list of genes. Currently accepts RefSeq.", required = false)
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File refSeqGeneList = null;
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/**
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* The format of the output file
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*/
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@Argument(fullName = "outputFormat", doc = "the format of the output file (e.g. csv, table, rtable); defaults to r-readable table", required = false)
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String outputFormat = "rtable";
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/**
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* A coverage threshold for summarizing (e.g. % bases >= CT for each sample)
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*/
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@Argument(fullName = "summaryCoverageThreshold", shortName = "ct", doc = "for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments.", required = false)
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int[] coverageThresholds = {15};
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@ -963,4 +1003,4 @@ class CoveragePartitioner {
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public Map<DoCOutputType.Partition,List<String>> getIdentifiersByType() {
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return identifiersByType;
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}
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}
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}
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|
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@ -0,0 +1,101 @@
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package org.broadinstitute.sting.gatk.walkers.diagnostics;
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import net.sf.samtools.SAMReadGroupRecord;
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
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import org.broadinstitute.sting.gatk.report.GATKReport;
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import org.broadinstitute.sting.gatk.report.GATKReportTable;
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import org.broadinstitute.sting.gatk.walkers.ReadWalker;
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import java.io.PrintStream;
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import java.util.List;
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/**
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* Outputs the read lengths of all the reads in a file.
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*
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* <p>
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* Generates a table with the read lengths categorized per sample. If the file has no sample information
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* (no read groups) it considers all reads to come from the same sample.
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* </p>
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*
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*
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* <h2>Input</h2>
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* <p>
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* A BAM file.
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* </p>
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*
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* <h2>Output</h2>
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* <p>
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* A human/R readable table of tab separated values with one column per sample and one row per read.
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* </p>
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*
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* <h2>Examples</h2>
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* <pre>
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* java
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* -jar GenomeAnalysisTK.jar
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* -T ReadLengthDistribution
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* -I example.bam
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* -R reference.fasta
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* -o example.tbl
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* </pre>
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*
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* @author Kiran Garimela
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*/
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||||
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||||
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public class ReadLengthDistribution extends ReadWalker<Integer, Integer> {
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@Output
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public PrintStream out;
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private GATKReport report;
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public void initialize() {
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report = new GATKReport();
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report.addTable("ReadLengthDistribution", "Table of read length distributions");
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GATKReportTable table = report.getTable("ReadLengthDistribution");
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table.addPrimaryKey("readLength");
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List<SAMReadGroupRecord> readGroups = getToolkit().getSAMFileHeader().getReadGroups();
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if (readGroups.isEmpty())
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table.addColumn("SINGLE_SAMPLE", 0);
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else
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for (SAMReadGroupRecord rg : readGroups)
|
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table.addColumn(rg.getSample(), 0);
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||||
|
||||
}
|
||||
|
||||
public boolean filter(ReferenceContext ref, SAMRecord read) {
|
||||
return ( !read.getReadPairedFlag() || read.getReadPairedFlag() && read.getFirstOfPairFlag());
|
||||
}
|
||||
|
||||
@Override
|
||||
public Integer map(ReferenceContext referenceContext, SAMRecord samRecord, ReadMetaDataTracker readMetaDataTracker) {
|
||||
GATKReportTable table = report.getTable("ReadLengthDistribution");
|
||||
|
||||
int length = Math.abs(samRecord.getReadLength());
|
||||
String sample = samRecord.getReadGroup().getSample();
|
||||
|
||||
table.increment(length, sample);
|
||||
|
||||
return null;
|
||||
}
|
||||
|
||||
@Override
|
||||
public Integer reduceInit() {
|
||||
return null;
|
||||
}
|
||||
|
||||
@Override
|
||||
public Integer reduce(Integer integer, Integer integer1) {
|
||||
return null;
|
||||
}
|
||||
|
||||
public void onTraversalDone(Integer sum) {
|
||||
report.print(out);
|
||||
}
|
||||
}
|
||||
|
|
@ -52,6 +52,11 @@ public class UnifiedArgumentCollection {
|
|||
@Argument(fullName = "heterozygosity", shortName = "hets", doc = "Heterozygosity value used to compute prior likelihoods for any locus", required = false)
|
||||
public Double heterozygosity = DiploidSNPGenotypePriors.HUMAN_HETEROZYGOSITY;
|
||||
|
||||
/**
|
||||
* The PCR error rate is independent of the sequencing error rate, which is necessary because we cannot necessarily
|
||||
* distinguish between PCR errors vs. sequencing errors. The practical implication for this value is that it
|
||||
* effectively acts as a cap on the base qualities.
|
||||
*/
|
||||
@Argument(fullName = "pcr_error_rate", shortName = "pcr_error", doc = "The PCR error rate to be used for computing fragment-based likelihoods", required = false)
|
||||
public Double PCR_error = DiploidSNPGenotypeLikelihoods.DEFAULT_PCR_ERROR_RATE;
|
||||
|
||||
|
|
|
|||
|
|
@ -77,6 +77,11 @@ import java.util.*;
|
|||
* if even a weak evidence for the same indel, not necessarily a confident call, exists in the first sample ("Normal"), or as somatic
|
||||
* if first bam has coverage at the site but no indication for an indel. In the --somatic mode, BED output contains
|
||||
* only somatic calls, while --verbose output contains all calls annotated with GERMLINE/SOMATIC keywords.
|
||||
*
|
||||
* <b>If any of the general usage of this tool or any of the command-line arguments for this tool are not clear to you,
|
||||
* please email asivache at broadinstitute dot org and he will gladly explain everything in more detail.</b>
|
||||
*
|
||||
*
|
||||
*/
|
||||
@ReadFilters({Platform454Filter.class, MappingQualityZeroFilter.class, PlatformUnitFilter.class})
|
||||
public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
|
||||
|
|
|
|||
|
|
@ -253,6 +253,13 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
|
|||
@Argument(fullName ="sample", shortName ="sn", doc="Name of the sample to validate (in case your VCF/BAM has more than one sample)", required=false)
|
||||
private String sample = "";
|
||||
|
||||
/**
|
||||
* Print out discordance sites to standard out.
|
||||
*/
|
||||
@Hidden
|
||||
@Argument(fullName ="print_interesting_sites", shortName ="print_interesting", doc="Print out interesting sites to standard out", required=false)
|
||||
private boolean printInterestingSites;
|
||||
|
||||
private UnifiedGenotyperEngine snpEngine;
|
||||
private UnifiedGenotyperEngine indelEngine;
|
||||
|
||||
|
|
@ -301,7 +308,12 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
|
|||
UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
|
||||
uac.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES;
|
||||
uac.alleles = alleles;
|
||||
if (!bamIsTruth) uac.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
|
||||
|
||||
// TODO -- if we change this tool to actually validate against the called allele, then this if statement is needed;
|
||||
// TODO -- for now, though, we need to be able to validate the right allele (because we only test isVariant below) [EB]
|
||||
//if (!bamIsTruth)
|
||||
uac.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
|
||||
|
||||
if (mbq >= 0) uac.MIN_BASE_QUALTY_SCORE = mbq;
|
||||
if (deletions >= 0)
|
||||
uac.MAX_DELETION_FRACTION = deletions;
|
||||
|
|
@ -371,19 +383,26 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
|
|||
if (call.isVariant()) {
|
||||
if (vcComp.isVariant())
|
||||
counter.nAltCalledAlt = 1L; // todo -- may wanna check if the alts called are the same?
|
||||
else
|
||||
else {
|
||||
counter.nAltCalledRef = 1L;
|
||||
if ( printInterestingSites )
|
||||
System.out.println("Truth=ALT Call=REF at " + call.getChr() + ":" + call.getStart());
|
||||
}
|
||||
}
|
||||
// If truth is a confident ALT call
|
||||
else {
|
||||
if (vcComp.isVariant())
|
||||
if (vcComp.isVariant()) {
|
||||
counter.nRefCalledAlt = 1L;
|
||||
else
|
||||
if ( printInterestingSites )
|
||||
System.out.println("Truth=REF Call=ALT at " + call.getChr() + ":" + call.getStart());
|
||||
} else
|
||||
counter.nRefCalledRef = 1L;
|
||||
}
|
||||
}
|
||||
else {
|
||||
counter.nNotConfidentCalls = 1L;
|
||||
if ( printInterestingSites )
|
||||
System.out.println("Truth is not confident at " + call.getChr() + ":" + call.getStart());
|
||||
writeVariant = false;
|
||||
}
|
||||
}
|
||||
|
|
@ -396,17 +415,24 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
|
|||
if (call.isCalledAlt(callConf)) {
|
||||
if (vcComp.getAttribute("GV").equals("T"))
|
||||
counter.nAltCalledAlt = 1L;
|
||||
else
|
||||
else {
|
||||
counter.nRefCalledAlt = 1L;
|
||||
if ( printInterestingSites )
|
||||
System.out.println("Truth=REF Call=ALT at " + call.getChr() + ":" + call.getStart());
|
||||
}
|
||||
}
|
||||
else if (call.isCalledRef(callConf)) {
|
||||
if (vcComp.getAttribute("GV").equals("T"))
|
||||
if (vcComp.getAttribute("GV").equals("T")) {
|
||||
counter.nAltCalledRef = 1L;
|
||||
else
|
||||
if ( printInterestingSites )
|
||||
System.out.println("Truth=ALT Call=REF at " + call.getChr() + ":" + call.getStart());
|
||||
} else
|
||||
counter.nRefCalledRef = 1L;
|
||||
}
|
||||
else {
|
||||
counter.nNotConfidentCalls = 1L;
|
||||
if ( printInterestingSites )
|
||||
System.out.println("Truth is not confident at " + call.getChr() + ":" + call.getStart());
|
||||
writeVariant = false;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -93,20 +93,30 @@ import java.util.List;
|
|||
*/
|
||||
@Requires(value={DataSource.REFERENCE})
|
||||
public class ValidationAmplicons extends RodWalker<Integer,Integer> {
|
||||
/**
|
||||
* A Table-formatted file listing amplicon contig, start, stop, and a name for the amplicon (or probe)
|
||||
*/
|
||||
@Input(fullName = "ProbeIntervals", doc="A collection of intervals in table format with optional names that represent the "+
|
||||
"intervals surrounding the probe sites amplicons should be designed for", required=true)
|
||||
RodBinding<TableFeature> probeIntervals;
|
||||
|
||||
/**
|
||||
* A VCF file containing the bi-allelic sites for validation. Filtered records will prompt a warning, and will be flagged as filtered in the output fastq.
|
||||
*/
|
||||
@Input(fullName = "ValidateAlleles", doc="A VCF containing the sites and alleles you want to validate. Restricted to *BI-Allelic* sites", required=true)
|
||||
RodBinding<VariantContext> validateAlleles;
|
||||
|
||||
/**
|
||||
* A VCF file containing variants to be masked. A mask variant overlapping a validation site will be ignored at the validation site.
|
||||
*/
|
||||
@Input(fullName = "MaskAlleles", doc="A VCF containing the sites you want to MASK from the designed amplicon (e.g. by Ns or lower-cased bases)", required=true)
|
||||
RodBinding<VariantContext> maskAlleles;
|
||||
|
||||
|
||||
@Argument(doc="Lower case SNPs rather than replacing with 'N'",fullName="lowerCaseSNPs",required=false)
|
||||
boolean lowerCaseSNPs = false;
|
||||
|
||||
/**
|
||||
* BWA single-end alignment is used as a primer specificity proxy. Low-complexity regions (that don't align back to themselves as a best hit) are lowercased.
|
||||
* This changes the size of the k-mer used for alignment.
|
||||
*/
|
||||
@Argument(doc="Size of the virtual primer to use for lower-casing regions with low specificity",fullName="virtualPrimerSize",required=false)
|
||||
int virtualPrimerSize = 20;
|
||||
|
||||
|
|
|
|||
|
|
@ -122,9 +122,6 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
|
|||
@Argument(fullName="doNotUseAllStandardStratifications", shortName="noST", doc="Do not use the standard stratification modules by default (instead, only those that are specified with the -S option)", required=false)
|
||||
protected Boolean NO_STANDARD_STRATIFICATIONS = false;
|
||||
|
||||
@Argument(fullName="onlyVariantsOfType", shortName="VT", doc="If provided, only variants of these types will be considered during the evaluation, in ", required=false)
|
||||
protected Set<VariantContext.Type> typesToUse = null;
|
||||
|
||||
/**
|
||||
* See the -list argument to view available modules.
|
||||
*/
|
||||
|
|
@ -317,9 +314,9 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
|
|||
// find the comp
|
||||
final VariantContext comp = findMatchingComp(eval, compSet);
|
||||
|
||||
HashMap<VariantStratifier, ArrayList<String>> stateMap = new HashMap<VariantStratifier, ArrayList<String>>();
|
||||
HashMap<VariantStratifier, List<String>> stateMap = new HashMap<VariantStratifier, List<String>>();
|
||||
for ( VariantStratifier vs : stratificationObjects ) {
|
||||
ArrayList<String> states = vs.getRelevantStates(ref, tracker, comp, compRod.getName(), eval, evalRod.getName(), sampleName);
|
||||
List<String> states = vs.getRelevantStates(ref, tracker, comp, compRod.getName(), eval, evalRod.getName(), sampleName);
|
||||
stateMap.put(vs, states);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -10,10 +10,13 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
|||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
/**
|
||||
* Stratifies the eval RODs by the allele count of the alternate allele
|
||||
*
|
||||
* Looks at the AC value in the INFO field, and uses that value if present. If absent,
|
||||
* computes the AC from the genotypes themselves. For no AC can be computed, 0 is used.
|
||||
*/
|
||||
public class AlleleCount extends VariantStratifier {
|
||||
// needs to know the variant context
|
||||
private ArrayList<String> states = new ArrayList<String>();
|
||||
|
||||
@Override
|
||||
public void initialize() {
|
||||
List<RodBinding<VariantContext>> evals = getVariantEvalWalker().getEvals();
|
||||
|
|
@ -35,11 +38,7 @@ public class AlleleCount extends VariantStratifier {
|
|||
getVariantEvalWalker().getLogger().info("AlleleCount using " + nchrom + " chromosomes");
|
||||
}
|
||||
|
||||
public ArrayList<String> getAllStates() {
|
||||
return states;
|
||||
}
|
||||
|
||||
public ArrayList<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
public List<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
ArrayList<String> relevantStates = new ArrayList<String>(1);
|
||||
|
||||
if (eval != null) {
|
||||
|
|
|
|||
|
|
@ -6,11 +6,15 @@ import org.broadinstitute.sting.utils.MathUtils;
|
|||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
/**
|
||||
* Stratifies the eval RODs by the allele frequency of the alternate allele
|
||||
*
|
||||
* Uses a constant 0.005 frequency grid, and projects the AF INFO field value. Requires
|
||||
* that AF be present in every ROD, otherwise this stratification throws an exception
|
||||
*/
|
||||
public class AlleleFrequency extends VariantStratifier {
|
||||
// needs to know the variant context
|
||||
private ArrayList<String> states;
|
||||
|
||||
@Override
|
||||
public void initialize() {
|
||||
states = new ArrayList<String>();
|
||||
|
|
@ -19,11 +23,7 @@ public class AlleleFrequency extends VariantStratifier {
|
|||
}
|
||||
}
|
||||
|
||||
public ArrayList<String> getAllStates() {
|
||||
return states;
|
||||
}
|
||||
|
||||
public ArrayList<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
public List<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
ArrayList<String> relevantStates = new ArrayList<String>();
|
||||
|
||||
if (eval != null) {
|
||||
|
|
|
|||
|
|
@ -6,22 +6,21 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
|||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
|
||||
/**
|
||||
* Required stratification grouping output by each comp ROD
|
||||
*/
|
||||
public class CompRod extends VariantStratifier implements RequiredStratification {
|
||||
private ArrayList<String> states;
|
||||
|
||||
@Override
|
||||
public void initialize() {
|
||||
states = new ArrayList<String>();
|
||||
for ( RodBinding<VariantContext> rod : getVariantEvalWalker().getComps() )
|
||||
states.add(rod.getName());
|
||||
}
|
||||
|
||||
public ArrayList<String> getAllStates() {
|
||||
return states;
|
||||
}
|
||||
|
||||
public ArrayList<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
public List<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
ArrayList<String> relevantStates = new ArrayList<String>();
|
||||
|
||||
relevantStates.add(compName);
|
||||
|
|
|
|||
|
|
@ -5,23 +5,19 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
|||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
/**
|
||||
* Stratifies the evaluation by each contig in the reference sequence
|
||||
*/
|
||||
public class Contig extends VariantStratifier {
|
||||
// needs to know the variant context
|
||||
private ArrayList<String> states;
|
||||
|
||||
@Override
|
||||
public void initialize() {
|
||||
states = new ArrayList<String>();
|
||||
states.addAll(getVariantEvalWalker().getContigNames());
|
||||
states.add("all");
|
||||
}
|
||||
|
||||
public ArrayList<String> getAllStates() {
|
||||
return states;
|
||||
}
|
||||
|
||||
public ArrayList<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
public List<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
ArrayList<String> relevantStates = new ArrayList<String>();
|
||||
|
||||
if (eval != null) {
|
||||
|
|
|
|||
|
|
@ -5,6 +5,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
|||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
/**
|
||||
* CpG is a stratification module for VariantEval that divides the input data by within/not within a CpG site
|
||||
|
|
@ -19,21 +20,14 @@ import java.util.ArrayList;
|
|||
* A CpG site is defined as a site where the reference base at a locus is a C and the adjacent reference base in the 3' direction is a G.
|
||||
*/
|
||||
public class CpG extends VariantStratifier {
|
||||
private ArrayList<String> states;
|
||||
|
||||
@Override
|
||||
public void initialize() {
|
||||
states = new ArrayList<String>();
|
||||
states.add("all");
|
||||
states.add("CpG");
|
||||
states.add("non_CpG");
|
||||
}
|
||||
|
||||
public ArrayList<String> getAllStates() {
|
||||
return states;
|
||||
}
|
||||
|
||||
public ArrayList<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
public List<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
boolean isCpG = false;
|
||||
if (ref != null && ref.getBases() != null) {
|
||||
String fwRefBases = new String(ref.getBases());
|
||||
|
|
|
|||
|
|
@ -7,10 +7,12 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
|||
import java.util.ArrayList;
|
||||
import java.util.HashMap;
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
|
||||
/**
|
||||
* Experimental stratification by the degeneracy of an amino acid, according to VCF annotation. Not safe
|
||||
*/
|
||||
public class Degeneracy extends VariantStratifier {
|
||||
private ArrayList<String> states;
|
||||
|
||||
private HashMap<String, HashMap<Integer, String>> degeneracies;
|
||||
|
||||
@Override
|
||||
|
|
@ -77,11 +79,7 @@ public class Degeneracy extends VariantStratifier {
|
|||
}
|
||||
}
|
||||
|
||||
public ArrayList<String> getAllStates() {
|
||||
return states;
|
||||
}
|
||||
|
||||
public ArrayList<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
public List<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
ArrayList<String> relevantStates = new ArrayList<String>();
|
||||
|
||||
relevantStates.add("all");
|
||||
|
|
|
|||
|
|
@ -6,10 +6,12 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
|||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
/**
|
||||
* Required stratification grouping output by each eval ROD
|
||||
*/
|
||||
public class EvalRod extends VariantStratifier implements RequiredStratification {
|
||||
private ArrayList<String> states;
|
||||
|
||||
@Override
|
||||
public void initialize() {
|
||||
states = new ArrayList<String>();
|
||||
|
|
@ -17,11 +19,7 @@ public class EvalRod extends VariantStratifier implements RequiredStratification
|
|||
states.add(rod.getName());
|
||||
}
|
||||
|
||||
public ArrayList<String> getAllStates() {
|
||||
return states;
|
||||
}
|
||||
|
||||
public ArrayList<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
public List<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
ArrayList<String> relevantStates = new ArrayList<String>();
|
||||
|
||||
relevantStates.add(evalName);
|
||||
|
|
|
|||
|
|
@ -5,24 +5,20 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
|||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
/**
|
||||
* Stratifies by the FILTER status (PASS, FAIL) of the eval records
|
||||
*/
|
||||
public class Filter extends VariantStratifier {
|
||||
// needs to know the variant context
|
||||
private ArrayList<String> states;
|
||||
|
||||
@Override
|
||||
public void initialize() {
|
||||
states = new ArrayList<String>();
|
||||
states.add("called");
|
||||
states.add("filtered");
|
||||
states.add("raw");
|
||||
}
|
||||
|
||||
public ArrayList<String> getAllStates() {
|
||||
return states;
|
||||
}
|
||||
|
||||
public ArrayList<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
public List<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
ArrayList<String> relevantStates = new ArrayList<String>();
|
||||
|
||||
relevantStates.add("raw");
|
||||
|
|
|
|||
|
|
@ -5,25 +5,22 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
|||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
/**
|
||||
* Stratifies by nonsense, missense, silent, and all annotations in the input ROD, from the INFO field annotation.
|
||||
*/
|
||||
public class FunctionalClass extends VariantStratifier {
|
||||
// needs to know the variant context
|
||||
private ArrayList<String> states;
|
||||
|
||||
@Override
|
||||
public void initialize() {
|
||||
states = new ArrayList<String>();
|
||||
states.add("all");
|
||||
states.add("silent");
|
||||
states.add("missense");
|
||||
states.add("nonsense");
|
||||
}
|
||||
|
||||
public ArrayList<String> getAllStates() {
|
||||
return states;
|
||||
}
|
||||
|
||||
public ArrayList<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
public List<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
ArrayList<String> relevantStates = new ArrayList<String>();
|
||||
|
||||
relevantStates.add("all");
|
||||
|
|
|
|||
|
|
@ -6,30 +6,30 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatc
|
|||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
|
||||
|
||||
import java.util.List;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Set;
|
||||
|
||||
/**
|
||||
* Stratifies the eval RODs by user-supplied JEXL expressions
|
||||
*
|
||||
* See http://www.broadinstitute.org/gsa/wiki/index.php/Using_JEXL_expressions for more details
|
||||
*/
|
||||
public class JexlExpression extends VariantStratifier implements StandardStratification {
|
||||
// needs to know the jexl expressions
|
||||
private Set<SortableJexlVCMatchExp> jexlExpressions;
|
||||
private ArrayList<String> states;
|
||||
|
||||
@Override
|
||||
public void initialize() {
|
||||
jexlExpressions = getVariantEvalWalker().getJexlExpressions();
|
||||
|
||||
states = new ArrayList<String>();
|
||||
states.add("none");
|
||||
for ( SortableJexlVCMatchExp jexlExpression : jexlExpressions ) {
|
||||
states.add(jexlExpression.name);
|
||||
}
|
||||
}
|
||||
|
||||
public ArrayList<String> getAllStates() {
|
||||
return states;
|
||||
}
|
||||
|
||||
public ArrayList<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
public List<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
ArrayList<String> relevantStates = new ArrayList<String>();
|
||||
relevantStates.add("none");
|
||||
|
||||
|
|
|
|||
|
|
@ -7,32 +7,31 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
|||
|
||||
import java.util.*;
|
||||
|
||||
/**
|
||||
* Stratifies by whether a site in in the list of known RODs (e.g., dbsnp by default)
|
||||
*/
|
||||
public class Novelty extends VariantStratifier implements StandardStratification {
|
||||
// needs the variant contexts and known names
|
||||
private List<RodBinding<VariantContext>> knowns;
|
||||
final private ArrayList<String> states = new ArrayList<String>(Arrays.asList("all", "known", "novel"));
|
||||
|
||||
|
||||
@Override
|
||||
public void initialize() {
|
||||
states = new ArrayList<String>(Arrays.asList("all", "known", "novel"));
|
||||
knowns = getVariantEvalWalker().getKnowns();
|
||||
}
|
||||
|
||||
public ArrayList<String> getAllStates() {
|
||||
return states;
|
||||
}
|
||||
|
||||
public ArrayList<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
public List<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
if (tracker != null && eval != null) {
|
||||
final Collection<VariantContext> knownComps = tracker.getValues(knowns, ref.getLocus());
|
||||
for ( final VariantContext c : knownComps ) {
|
||||
// loop over sites, looking for something that matches the type eval
|
||||
if ( eval.getType() == c.getType() ) {
|
||||
return new ArrayList<String>(Arrays.asList("all", "known"));
|
||||
return Arrays.asList("all", "known");
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return new ArrayList<String>(Arrays.asList("all", "novel"));
|
||||
return Arrays.asList("all", "novel");
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -4,26 +4,23 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
|||
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
||||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
|
||||
/**
|
||||
* Stratifies the eval RODs by each sample in the eval ROD.
|
||||
*
|
||||
* This allows the system to analyze each sample separately. Since many evaluations
|
||||
* only consider non-reference sites, stratifying by sample results in meaningful
|
||||
* calculations for CompOverlap
|
||||
*/
|
||||
public class Sample extends VariantStratifier {
|
||||
// needs the sample names
|
||||
private ArrayList<String> samples;
|
||||
|
||||
@Override
|
||||
public void initialize() {
|
||||
samples = new ArrayList<String>();
|
||||
samples.addAll(getVariantEvalWalker().getSampleNamesForStratification());
|
||||
states.addAll(getVariantEvalWalker().getSampleNamesForStratification());
|
||||
}
|
||||
|
||||
public ArrayList<String> getAllStates() {
|
||||
return samples;
|
||||
}
|
||||
|
||||
public ArrayList<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
ArrayList<String> relevantStates = new ArrayList<String>();
|
||||
relevantStates.add(sampleName);
|
||||
|
||||
return relevantStates;
|
||||
public List<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
return Arrays.asList(sampleName);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -6,9 +6,12 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
|
|||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
|
||||
public abstract class VariantStratifier implements Comparable {
|
||||
private VariantEvalWalker variantEvalWalker;
|
||||
protected ArrayList<String> states = new ArrayList<String>();
|
||||
|
||||
/**
|
||||
* @return a reference to the parent VariantEvalWalker running this stratification
|
||||
|
|
@ -27,15 +30,15 @@ public abstract class VariantStratifier implements Comparable {
|
|||
|
||||
public abstract void initialize();
|
||||
|
||||
public ArrayList<String> getAllStates() {
|
||||
return new ArrayList<String>();
|
||||
}
|
||||
|
||||
public ArrayList<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
public List<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
return null;
|
||||
}
|
||||
|
||||
public int compareTo(Object o1) {
|
||||
return this.getClass().getSimpleName().compareTo(o1.getClass().getSimpleName());
|
||||
}
|
||||
|
||||
public ArrayList<String> getAllStates() {
|
||||
return states;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,49 @@
|
|||
/*
|
||||
* Copyright (c) 2011, The Broad Institute
|
||||
*
|
||||
* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* files (the "Software"), to deal in the Software without
|
||||
* restriction, including without limitation the rights to use,
|
||||
* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||
* copies of the Software, and to permit persons to whom the
|
||||
* Software is furnished to do so, subject to the following
|
||||
* conditions:
|
||||
*
|
||||
* The above copyright notice and this permission notice shall be
|
||||
* included in all copies or substantial portions of the Software.
|
||||
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
||||
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
||||
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
||||
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
||||
* OTHER DEALINGS IN THE SOFTWARE.
|
||||
*/
|
||||
|
||||
package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
|
||||
|
||||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
||||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.Collections;
|
||||
import java.util.List;
|
||||
|
||||
/**
|
||||
* Stratifies the eval variants by their type (SNP, INDEL, ETC)
|
||||
*/
|
||||
public class VariantType extends VariantStratifier {
|
||||
@Override
|
||||
public void initialize() {
|
||||
for ( VariantContext.Type t : VariantContext.Type.values() ) {
|
||||
states.add(t.toString());
|
||||
}
|
||||
}
|
||||
|
||||
public List<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
|
||||
return eval == null ? Collections.<String>emptyList() : Arrays.asList(eval.getType().toString());
|
||||
}
|
||||
}
|
||||
|
|
@ -266,10 +266,7 @@ public class VariantEvalUtils {
|
|||
* @return a new VariantContext with just the requested sample
|
||||
*/
|
||||
public VariantContext getSubsetOfVariantContext(VariantContext vc, String sampleName) {
|
||||
ArrayList<String> sampleNames = new ArrayList<String>();
|
||||
sampleNames.add(sampleName);
|
||||
|
||||
return getSubsetOfVariantContext(vc, sampleNames);
|
||||
return getSubsetOfVariantContext(vc, Arrays.asList(sampleName));
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -280,7 +277,7 @@ public class VariantEvalUtils {
|
|||
* @return a new VariantContext with just the requested samples
|
||||
*/
|
||||
public VariantContext getSubsetOfVariantContext(VariantContext vc, Collection<String> sampleNames) {
|
||||
VariantContext vcsub = vc.subContextFromGenotypes(vc.getGenotypes(sampleNames).values(), vc.getAlleles());
|
||||
VariantContext vcsub = vc.subContextFromGenotypes(vc.getGenotypes(sampleNames).values());
|
||||
|
||||
HashMap<String, Object> newAts = new HashMap<String, Object>(vcsub.getAttributes());
|
||||
|
||||
|
|
@ -371,12 +368,12 @@ public class VariantEvalUtils {
|
|||
* @param stateKeys all the state keys
|
||||
* @return a list of state keys
|
||||
*/
|
||||
public ArrayList<StateKey> initializeStateKeys(HashMap<VariantStratifier, ArrayList<String>> stateMap, Stack<HashMap<VariantStratifier, ArrayList<String>>> stateStack, StateKey stateKey, ArrayList<StateKey> stateKeys) {
|
||||
public ArrayList<StateKey> initializeStateKeys(HashMap<VariantStratifier, List<String>> stateMap, Stack<HashMap<VariantStratifier, List<String>>> stateStack, StateKey stateKey, ArrayList<StateKey> stateKeys) {
|
||||
if (stateStack == null) {
|
||||
stateStack = new Stack<HashMap<VariantStratifier, ArrayList<String>>>();
|
||||
stateStack = new Stack<HashMap<VariantStratifier, List<String>>>();
|
||||
|
||||
for (VariantStratifier vs : stateMap.keySet()) {
|
||||
HashMap<VariantStratifier, ArrayList<String>> oneSetOfStates = new HashMap<VariantStratifier, ArrayList<String>>();
|
||||
HashMap<VariantStratifier, List<String>> oneSetOfStates = new HashMap<VariantStratifier, List<String>>();
|
||||
oneSetOfStates.put(vs, stateMap.get(vs));
|
||||
|
||||
stateStack.add(oneSetOfStates);
|
||||
|
|
@ -384,10 +381,10 @@ public class VariantEvalUtils {
|
|||
}
|
||||
|
||||
if (!stateStack.isEmpty()) {
|
||||
Stack<HashMap<VariantStratifier, ArrayList<String>>> newStateStack = new Stack<HashMap<VariantStratifier, ArrayList<String>>>();
|
||||
Stack<HashMap<VariantStratifier, List<String>>> newStateStack = new Stack<HashMap<VariantStratifier, List<String>>>();
|
||||
newStateStack.addAll(stateStack);
|
||||
|
||||
HashMap<VariantStratifier, ArrayList<String>> oneSetOfStates = newStateStack.pop();
|
||||
HashMap<VariantStratifier, List<String>> oneSetOfStates = newStateStack.pop();
|
||||
VariantStratifier vs = oneSetOfStates.keySet().iterator().next();
|
||||
|
||||
for (String state : oneSetOfStates.get(vs)) {
|
||||
|
|
|
|||
|
|
@ -214,7 +214,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
|
|||
@Argument(fullName="sample_expressions", shortName="se", doc="Regular expression to select many samples from the ROD tracks provided. Can be specified multiple times", required=false)
|
||||
public Set<String> sampleExpressions ;
|
||||
|
||||
@Argument(fullName="sample_file", shortName="sf", doc="File containing a list of samples (one per line) to include. Can be specified multiple times", required=false)
|
||||
@Input(fullName="sample_file", shortName="sf", doc="File containing a list of samples (one per line) to include. Can be specified multiple times", required=false)
|
||||
public Set<File> sampleFiles;
|
||||
|
||||
/**
|
||||
|
|
@ -226,7 +226,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
|
|||
/**
|
||||
* Note that sample exclusion takes precedence over inclusion, so that if a sample is in both lists it will be excluded.
|
||||
*/
|
||||
@Argument(fullName="exclude_sample_file", shortName="xl_sf", doc="File containing a list of samples (one per line) to exclude. Can be specified multiple times", required=false)
|
||||
@Input(fullName="exclude_sample_file", shortName="xl_sf", doc="File containing a list of samples (one per line) to exclude. Can be specified multiple times", required=false)
|
||||
public Set<File> XLsampleFiles = new HashSet<File>(0);
|
||||
|
||||
/**
|
||||
|
|
|
|||
|
|
@ -26,7 +26,6 @@
|
|||
package org.broadinstitute.sting.gatk.walkers.variantutils;
|
||||
|
||||
import org.broad.tribble.TribbleException;
|
||||
import org.broad.tribble.dbsnp.DbSNPFeature;
|
||||
import org.broadinstitute.sting.commandline.*;
|
||||
import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
|
||||
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
|
||||
|
|
@ -41,7 +40,6 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
|||
import java.io.File;
|
||||
import java.util.Collection;
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
import java.util.Set;
|
||||
|
||||
|
||||
|
|
@ -168,14 +166,9 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
|
|||
// get the RS IDs
|
||||
Set<String> rsIDs = null;
|
||||
if ( tracker.hasValues(dbsnp.dbsnp) ) {
|
||||
List<VariantContext> dbsnpList = tracker.getValues(dbsnp.dbsnp, ref.getLocus());
|
||||
rsIDs = new HashSet<String>();
|
||||
for ( Object d : dbsnpList ) {
|
||||
if (d instanceof DbSNPFeature )
|
||||
rsIDs.add(((DbSNPFeature)d).getRsID());
|
||||
else if (d instanceof VariantContext )
|
||||
rsIDs.add(((VariantContext)d).getID());
|
||||
}
|
||||
for ( VariantContext rsID : tracker.getValues(dbsnp.dbsnp, ref.getLocus()) )
|
||||
rsIDs.add(rsID.getID());
|
||||
}
|
||||
|
||||
try {
|
||||
|
|
|
|||
|
|
@ -252,7 +252,8 @@ public class ClippingOp {
|
|||
if (start == 0 && stop == read.getReadLength() -1)
|
||||
return new SAMRecord(read.getHeader());
|
||||
|
||||
CigarShift cigarShift = hardClipCigar(read.getCigar(), start, stop);
|
||||
// If the read is unmapped there is no Cigar string and neither should we create a new cigar string
|
||||
CigarShift cigarShift = (read.getReadUnmappedFlag()) ? new CigarShift(new Cigar(), 0, 0) : hardClipCigar(read.getCigar(), start, stop);
|
||||
|
||||
// the cigar may force a shift left or right (or both) in case we are left with insertions
|
||||
// starting or ending the read after applying the hard clip on start/stop.
|
||||
|
|
|
|||
|
|
@ -82,7 +82,7 @@ public class PileupElement {
|
|||
// --------------------------------------------------------------------------
|
||||
|
||||
private Integer getReducedReadQualityTagValue() {
|
||||
return (Integer)getRead().getAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG);
|
||||
return getRead().getIntegerAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG);
|
||||
}
|
||||
|
||||
public boolean isReducedRead() {
|
||||
|
|
|
|||
|
|
@ -41,6 +41,10 @@ public class GATKSAMRecord extends SAMRecord {
|
|||
// because some values can be null, we don't want to duplicate effort
|
||||
private boolean retrievedReadGroup = false;
|
||||
|
||||
/** A private cache for the reduced read quality. Null indicates the value hasn't be fetched yet or isn't available */
|
||||
private boolean lookedUpReducedReadQuality = false;
|
||||
private Integer reducedReadQuality;
|
||||
|
||||
// These temporary attributes were added here to make life easier for
|
||||
// certain algorithms by providing a way to label or attach arbitrary data to
|
||||
// individual GATKSAMRecords.
|
||||
|
|
@ -338,7 +342,17 @@ public class GATKSAMRecord extends SAMRecord {
|
|||
|
||||
public Object getAttribute(final String tag) { return mRecord.getAttribute(tag); }
|
||||
|
||||
public Integer getIntegerAttribute(final String tag) { return mRecord.getIntegerAttribute(tag); }
|
||||
public Integer getIntegerAttribute(final String tag) {
|
||||
if ( tag == ReadUtils.REDUCED_READ_QUALITY_TAG ) {
|
||||
if ( ! lookedUpReducedReadQuality ) {
|
||||
lookedUpReducedReadQuality = true;
|
||||
reducedReadQuality = mRecord.getIntegerAttribute(tag);
|
||||
}
|
||||
return reducedReadQuality;
|
||||
} else {
|
||||
return mRecord.getIntegerAttribute(tag);
|
||||
}
|
||||
}
|
||||
|
||||
public Short getShortAttribute(final String tag) { return mRecord.getShortAttribute(tag); }
|
||||
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
|
|||
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-R " + b36KGReference +
|
||||
" --variant:dbsnp " + GATKDataLocation + "Comparisons/Validated/dbSNP/dbsnp_129_b36.rod" +
|
||||
" --variant:OldDbsnp " + GATKDataLocation + "Comparisons/Validated/dbSNP/dbsnp_129_b36.rod" +
|
||||
" -T VariantsToVCF" +
|
||||
" -L 1:1-30,000,000" +
|
||||
" -o %s" +
|
||||
|
|
|
|||
|
|
@ -31,8 +31,8 @@ public class CachingIndexedFastaSequenceFileUnitTest extends BaseTest {
|
|||
private static final int STEP_SIZE = 1;
|
||||
|
||||
//private static final List<Integer> QUERY_SIZES = Arrays.asList(1);
|
||||
private static final List<Integer> QUERY_SIZES = Arrays.asList(1, 10, 100, 1000);
|
||||
private static final List<Integer> CACHE_SIZES = Arrays.asList(-1, 10, 1000);
|
||||
private static final List<Integer> QUERY_SIZES = Arrays.asList(1, 10, 100);
|
||||
private static final List<Integer> CACHE_SIZES = Arrays.asList(-1, 1000);
|
||||
|
||||
@DataProvider(name = "fastas")
|
||||
public Object[][] createData1() {
|
||||
|
|
|
|||
|
|
@ -11,7 +11,7 @@ import net.sf.samtools.SAMFileReader
|
|||
import net.sf.samtools.SAMFileHeader.SortOrder
|
||||
|
||||
import org.broadinstitute.sting.queue.util.QScriptUtils
|
||||
import org.broadinstitute.sting.queue.function.{CommandLineFunction, ListWriterFunction}
|
||||
import org.broadinstitute.sting.queue.function.ListWriterFunction
|
||||
|
||||
class DataProcessingPipeline extends QScript {
|
||||
qscript =>
|
||||
|
|
@ -31,7 +31,7 @@ class DataProcessingPipeline extends QScript {
|
|||
var reference: File = _
|
||||
|
||||
@Input(doc="dbsnp ROD to use (must be in VCF format)", fullName="dbsnp", shortName="D", required=true)
|
||||
var dbSNP: File = _
|
||||
var dbSNP: List[File] = List()
|
||||
|
||||
/****************************************************************************
|
||||
* Optional Parameters
|
||||
|
|
@ -43,7 +43,7 @@ class DataProcessingPipeline extends QScript {
|
|||
//
|
||||
|
||||
@Input(doc="extra VCF files to use as reference indels for Indel Realignment", fullName="extra_indels", shortName="indels", required=false)
|
||||
var indels: File = _
|
||||
var indels: List[File] = List()
|
||||
|
||||
@Input(doc="The path to the binary of bwa (usually BAM files have already been mapped - but if you want to remap this is the option)", fullName="path_to_bwa", shortName="bwa", required=false)
|
||||
var bwaPath: File = _
|
||||
|
|
@ -159,7 +159,7 @@ class DataProcessingPipeline extends QScript {
|
|||
for (rg <- readGroups) {
|
||||
val intermediateInBam: File = if (index == readGroups.length) { inBam } else { swapExt(outBam, ".bam", index+1 + "-rg.bam") }
|
||||
val intermediateOutBam: File = if (index > 1) {swapExt(outBam, ".bam", index + "-rg.bam") } else { outBam}
|
||||
val readGroup = new ReadGroup(rg.getReadGroupId, rg.getPlatform, rg.getLibrary, rg.getPlatformUnit, rg.getSample, rg.getSequencingCenter, rg.getDescription)
|
||||
val readGroup = new ReadGroup(rg.getReadGroupId, rg.getLibrary, rg.getPlatform, rg.getPlatformUnit, rg.getSample, rg.getSequencingCenter, rg.getDescription)
|
||||
add(addReadGroup(intermediateInBam, intermediateOutBam, readGroup))
|
||||
index = index - 1
|
||||
}
|
||||
|
|
@ -321,9 +321,9 @@ class DataProcessingPipeline extends QScript {
|
|||
this.input_file = inBams
|
||||
this.out = outIntervals
|
||||
this.mismatchFraction = 0.0
|
||||
this.known :+= qscript.dbSNP
|
||||
this.known ++= qscript.dbSNP
|
||||
if (indels != null)
|
||||
this.known :+= qscript.indels
|
||||
this.known ++= qscript.indels
|
||||
this.scatterCount = nContigs
|
||||
this.analysisName = queueLogDir + outIntervals + ".target"
|
||||
this.jobName = queueLogDir + outIntervals + ".target"
|
||||
|
|
@ -333,9 +333,9 @@ class DataProcessingPipeline extends QScript {
|
|||
this.input_file = inBams
|
||||
this.targetIntervals = tIntervals
|
||||
this.out = outBam
|
||||
this.known :+= qscript.dbSNP
|
||||
this.known ++= qscript.dbSNP
|
||||
if (qscript.indels != null)
|
||||
this.known :+= qscript.indels
|
||||
this.known ++= qscript.indels
|
||||
this.consensusDeterminationModel = cleanModelEnum
|
||||
this.compress = 0
|
||||
this.scatterCount = nContigs
|
||||
|
|
@ -344,7 +344,7 @@ class DataProcessingPipeline extends QScript {
|
|||
}
|
||||
|
||||
case class cov (inBam: File, outRecalFile: File) extends CountCovariates with CommandLineGATKArgs {
|
||||
this.knownSites :+= qscript.dbSNP
|
||||
this.knownSites ++= qscript.dbSNP
|
||||
this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
|
||||
this.input_file :+= inBam
|
||||
this.recal_file = outRecalFile
|
||||
|
|
|
|||
|
|
@ -1,6 +1,5 @@
|
|||
package org.broadinstitute.sting.queue.qscripts
|
||||
|
||||
import org.broadinstitute.sting.commandline.Hidden
|
||||
import org.broadinstitute.sting.queue.extensions.gatk._
|
||||
import org.broadinstitute.sting.queue.QScript
|
||||
import org.broadinstitute.sting.gatk.phonehome.GATKRunReport
|
||||
|
|
@ -70,7 +69,8 @@ class MethodsDevelopmentCallingPipeline extends QScript {
|
|||
val goldStandardClusterFile = new File(goldStandardName + ".clusters")
|
||||
}
|
||||
|
||||
val hg19 = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
|
||||
val b37_decoy = new File("/humgen/1kg/reference/human_g1k_v37_decoy.fasta")
|
||||
val hg19 = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
|
||||
val hg18 = new File("/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta")
|
||||
val b36 = new File("/humgen/1kg/reference/human_b36_both.fasta")
|
||||
val b37 = new File("/humgen/1kg/reference/human_g1k_v37.fasta")
|
||||
|
|
@ -124,6 +124,14 @@ class MethodsDevelopmentCallingPipeline extends QScript {
|
|||
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.bwa.cleaned.recal.bam"),
|
||||
new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
|
||||
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, 99.0, !lowPass, !exome, 3),
|
||||
"WExTrioDecoy" -> new Target("CEUTrio.HiSeq.WEx.b37_decoy", b37_decoy, dbSNP_b37, hapmap_b37, indelMask_b37,
|
||||
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WEx.b37_decoy.list"),
|
||||
new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
|
||||
"/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 3.3, 98.0, !lowPass, exome, 3),
|
||||
"WGSTrioDecoy" -> new Target("CEUTrio.HiSeq.WGS.b37_decoy", b37_decoy, dbSNP_b37, hapmap_b37, indelMask_b37,
|
||||
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.b37_decoy.list"),
|
||||
new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
|
||||
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, 99.0, !lowPass, !exome, 3),
|
||||
"FIN" -> new Target("FIN", b37, dbSNP_b37, hapmap_b37, indelMask_b37,
|
||||
new File("/humgen/1kg/processing/pipeline_test_bams/FIN.79sample.Nov2010.chr20.bam"),
|
||||
new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
|
||||
|
|
|
|||
|
|
@ -1,31 +1,14 @@
|
|||
<ivysettings>
|
||||
<properties file="${ivy.settings.dir}/ivysettings.properties"/>
|
||||
<settings defaultResolver="libraries"/>
|
||||
<settings defaultResolver="chain"/>
|
||||
<resolvers>
|
||||
<filesystem name="projects">
|
||||
<artifact pattern="${repository.dir}/[organisation]/[artifact]-[revision].[ext]" />
|
||||
<ivy pattern="${repository.dir}/[organisation]/[module]-[revision].xml" />
|
||||
</filesystem>
|
||||
<ibiblio name="libraries" m2compatible="true" />
|
||||
<ibiblio name="libraries_with_inconsistent_poms" checkconsistency="false" m2compatible="true" />
|
||||
<ibiblio name="reflections-repo" m2compatible="true" root="http://reflections.googlecode.com/svn/repo" />
|
||||
<ibiblio name="java.net" m2compatible="false" root="http://download.java.net/maven/1/" pattern="[organisation]/jars/[artifact]-[revision].[ext]"/>
|
||||
<ibiblio name="maven2-repository.dev.java.net" m2compatible="true" root="http://download.java.net/maven/2/" />
|
||||
<chain name="chain">
|
||||
<filesystem name="projects">
|
||||
<artifact pattern="${repository.dir}/[organisation]/[artifact]-[revision].[ext]" />
|
||||
<ivy pattern="${repository.dir}/[organisation]/[module]-[revision].xml" />
|
||||
</filesystem>
|
||||
<ibiblio name="reflections-repo" m2compatible="true" root="http://reflections.googlecode.com/svn/repo" />
|
||||
<ibiblio name="maven" root="http://repo1.maven.org/maven2" m2compatible="true" />
|
||||
</chain>
|
||||
</resolvers>
|
||||
<modules>
|
||||
<module organisation="edu.mit.broad" resolver="projects" />
|
||||
<module organisation="net.sf" module="functionalj" resolver="projects" />
|
||||
<module organisation="net.sf" module="samtools" resolver="projects" />
|
||||
<module organisation="org.reflections" module="reflections" resolver="reflections-repo" />
|
||||
<module organisation="org.broad" module="tribble" resolver="projects" />
|
||||
<module organisation="gov.nist" module="Jama" resolver="projects" />
|
||||
<!-- If colt fixes the version in the pom for 1.2.0 then this line can be removed. -->
|
||||
<module organisation="colt" module="colt" resolver="libraries_with_inconsistent_poms" />
|
||||
<module organisation="javax.mail" resolver="java.net" />
|
||||
<module organisation="javax.activation" resolver="java.net" />
|
||||
<module organisation="net.java.dev.jna" resolver="maven2-repository.dev.java.net" />
|
||||
<module organisation="com.google.code.caliper" resolver="projects" />
|
||||
<module organisation="net.sf.gridscheduler" resolver="projects" />
|
||||
<module organisation="com.google.code.cofoja" resolver="projects" />
|
||||
</modules>
|
||||
</ivysettings>
|
||||
|
|
|
|||
Binary file not shown.
|
|
@ -1,3 +1,3 @@
|
|||
<ivy-module version="1.0">
|
||||
<info organisation="org.broad" module="tribble" revision="21" status="integration" />
|
||||
<info organisation="org.broad" module="tribble" revision="24" status="integration" />
|
||||
</ivy-module>
|
||||
Loading…
Reference in New Issue